Selaginella apoda is the central component of a taxonomically difficult species complex of eastern North America. It is closely related to S . eclipes (see discussion) and S . ludoviciana . Naturally occurring and experimental hybrids between S . apoda and S . ludoviciana have been reported (P. Somers and W. R. Buck 1975; T. R. Webster 1990). Also, some evidence indicates that hybrids may occur between S . apoda and S . eclipes . More studies are needed in this complex.

The species in the S . apoda complex may be best classified under subg. Homostachys of J. G. Baker (1883, 1887), with which they share flattened strobili and larger sporophylls (megasporophylls) that are usually in the same plane as the vegetative lateral leaves. They are, however, treated here with the other heterophyllous species of subg. Stachygynandrum until a reassessment of the classification of the genus Selaginella can be made.